Human immunodeficiency virus (HIV) infection remains a significant public and global health threat. Our long-term goal is the development of small molecule fusion inhibitors to be used as anti-HIV therapeutics. The specific objective of this proposal is to generate new drug leads which bind tightly to a highly-conserved deep pocket formed by the gp41 N-heptad repeat trimer. Our central hypothesis is that known gp41 inhibitors (including small molecules and peptides) can act as reference molecules to facilitate and drive the discovery of new leads. The hypothesis is motivated in part by the Sponsor's Lab's development and application of a new receptor-based method (called per-residue footprint comparisons) which employed the known peptide inhibitor C34 to successfully identify small-molecule leads with gp41 activity. The present postdoctoral application emphasizes an orthogonal ligand-based approach which uses chemical information inherent to peptide inhibitors as well as reported small molecule inhibitors. Ligand properties including 2D fingerprint similarity, 3D pharmacophores, and volume overlap will be used to design new gp41 drug-lead candidates. The rationale for the proposed work is that the design of large ensembles of compounds with chemical properties tailored to a reference, or a combination of references, will enable discovery of new gp41 inhibitors as leads for development of anti-HIV therapeutics. The proposed research can be arranged as the following specific aims: 1) Construct new small-molecule gp41 inhibitors from scratch guided by cheminformatic and molecular properties of known small-molecule and peptide inhibitors, 2) Optimize functionality for select gp41 inhibitors (Holden et al., 2012) to maximize property overlap with available crystallographic peptide co-complexes, and 3) Establish quantitative-structure-activity-relationships with experiment for congeneric series of gp41 inhibitors reported in the literature (Zhou et al., 2010; Stewart et al., 2010; Jiang et al., 2011). Under the first aim, new small molecules will be constructed from building block libraries, guided by the chemical information inherent to known C-peptides and reported small molecule inhibitors. Under the second aim, known small molecule inhibitors will be improved through SAR modification of functional groups to more completely mimic key peptide side chain properties. Under the third aim, receptor-based docking will be employed to effectively identify low- energy ligand binding poses of known gp41 inhibitors, followed by molecular simulation to establish a quantitative correlation with experiment. This primarily ligand-based approach is innovative because it is designed to search a new area in chemical space and ultimately converge upon a distinct subset of potential fusion inhibitors targeting HIV gp41. The proposed research is significant because it is likely to aid in the development of new therapeutics for the treatment of HIV, ultimately contributing to the NIH's mission to enhance health, lengthen life, and reduce the burdens of illness and disability.